// Action_ClusterDihedral::ReadDihedrals()
int Action_ClusterDihedral::ReadDihedrals(std::string const& fname) {
CpptrajFile infile;
char buffer[256];
int a1, a2, a3, a4, bins;
double min;
if ( infile.OpenRead( fname ) ) return 1;
mprintf("\tReading dihedral information from %s\n", fname.c_str());
while (infile.Gets(buffer, 256)==0) {
// Expected line format: At#1 At#2 At#3 At#4 Bins Min
// ATOM NUMBERS SHOULD START FROM 1!
int nvals = sscanf(buffer, "%i %i %i %i %i %lf", &a1, &a2, &a3, &a4, &bins, &min);
if (nvals < 5) {
mprinterr("Error: Dihedral file %s: Expected at least 5 values, got %i\n",
fname.c_str(), nvals);
mprinterr("Error: Problem line: [%s]\n",buffer);
mprinterr("Error: Expected format: At#1 At#2 At#3 At#4 Bins [Min]\n");
return 1; // This should automatically close infile through destructor.
}
if (nvals < 6)
min = minimum_;
DCmasks_.push_back( DCmask(a1-1, a2-1, a3-1, a4-1, bins, min ) );
mprintf("\t\t(%i)-(%i)-(%i)-(%i) Bins=%i Min=%.3f\n",a1,a2,a3,a4,bins,min);
}
mprintf("\tRead %zu dihedrals.\n", DCmasks_.size());
infile.CloseFile();
return 0;
}
/** Header is 256 4-byte words. Integer unless otherwise noted. First 56 words are:
* 0-2: columns, rows, sections (fastest changing to slowest)
* 3: mode: 0 = envelope stored as signed bytes (from -128 lowest to 127 highest)
* 1 = Image stored as Integer*2
* 2 = Image stored as Reals
* 3 = Transform stored as Complex Integer*2
* 4 = Transform stored as Complex Reals
* 5 == 0
* 4-6: Column, row, and section offsets
* 7-9: Intervals along X, Y, Z
* 10-15: float; 3x cell lengths (Ang) and 3x cell angles (deg)
* 16-18: Map of which axes correspond to cols, rows, sections (1,2,3 = x,y,z)
* 19-21: float; Min, max, and mean density
* 22-24: Space group, bytes used for storing symm ops, flag for skew transform
* If skew flag != 0, skew transformation is from standard orthogonal
* coordinate frame (as used for atoms) to orthogonal map frame, as:
* Xo(map) = S * (Xo(atoms) - t)
* 25-33: Skew matrix 'S' (in order S11, S12, S13, S21 etc)
* 34-36: Skew translation 't'
* 37-51: For future use and can be skipped.
* 52: char; 'MAP '
* 53: char; machine stamp for determining endianness
* 54: float; RMS deviation of map from mean
* 55: Number of labels
*/
int DataIO_CCP4::ReadData(FileName const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
CpptrajFile infile;
if (infile.OpenRead( fname )) return 1;
// Read first 56 words of the header into a buffer.
headerbyte buffer;
if (infile.Read(buffer.i, 224*sizeof(unsigned char)) < 1) {
mprinterr("Error: Could not buffer CCP4 header.\n");
return 1;
}
if (debug_ > 0)
mprintf("DEBUG: MAP= '%c %c %c %c' MACHST= '%x %x %x %x'\n",
buffer.c[208], buffer.c[209], buffer.c[210], buffer.c[211],
buffer.c[212], buffer.c[213], buffer.c[214], buffer.c[215]);
// SANITY CHECK
if (!MapCharsValid(buffer.c + 208)) {
mprinterr("Error: CCP4 file missing 'MAP ' string at word 53\n");
return 1;
}
// Check endianess
bool isBigEndian = (buffer.c[212] == 0x11 && buffer.c[213] == 0x11 &&
buffer.c[214] == 0x00 && buffer.c[215] == 0x00);
if (!isBigEndian) {
if (debug_ > 0) mprintf("DEBUG: Little endian.\n");
// SANITY CHECK
if ( !(buffer.c[212] == 0x44 && buffer.c[213] == 0x41 &&
buffer.c[214] == 0x00 && buffer.c[215] == 0x00) )
mprintf("Warning: Invalid machine stamp: %x %x %x %x : assuming little endian.\n",
buffer.c[212], buffer.c[213], buffer.c[214], buffer.c[215]);
} else {
if (debug_ > 0) mprintf("DEBUG: Big endian.\n");
// Perform endian swapping on header if necessary
endian_swap(buffer.i, 56);
}
// Print DEBUG info
if (debug_ > 0) {
mprintf("DEBUG: Columns=%i Rows=%i Sections=%i\n", buffer.i[0], buffer.i[1], buffer.i[2]);
mprintf("DEBUG: Mode=%i\n", buffer.i[3]);
mprintf("DEBUG: Offsets: C=%i R=%i S=%i\n", buffer.i[4], buffer.i[5], buffer.i[6]);
mprintf("DEBUG: NXYZ={ %i %i %i }\n", buffer.i[7], buffer.i[8], buffer.i[9]);
mprintf("DEBUG: Box XYZ={ %f %f %f } ABG={ %f %f %f }\n",
buffer.f[10], buffer.f[11], buffer.f[12],
buffer.f[13], buffer.f[14], buffer.f[15]);
mprintf("DEBUG: Map: ColAxis=%i RowAxis=%i SecAxis=%i\n",
buffer.i[16], buffer.i[17], buffer.i[18]);
mprintf("DEBUG: SpaceGroup#=%i SymmOpBytes=%i SkewFlag=%i\n",
buffer.i[22], buffer.i[23], buffer.i[24]);
const int* MSKEW = buffer.i + 25;
mprintf("DEBUG: Skew matrix: %i %i %i\n"
" %i %i %i\n"
" %i %i %i\n", MSKEW[0], MSKEW[1], MSKEW[2], MSKEW[3],
MSKEW[4], MSKEW[5], MSKEW[6], MSKEW[7], MSKEW[8]);
const int* TSKEW = buffer.i + 34;
mprintf("DEBUG: Skew translation: %i %i %i\n", TSKEW[0], TSKEW[1], TSKEW[2]);
mprintf("DEBUG: Nlabels=%i\n", buffer.i[55]);
}
// Check input data. Only support mode 2 for now.
if (buffer.i[3] != 2) {
mprinterr("Error: Mode %i; currently only mode 2 for CCP4 files is supported.\n", buffer.i[3]);
return 1;
}
// Check offsets.
if (buffer.i[4] != 0 || buffer.i[5] != 0 || buffer.i[6] != 0)
mprintf("Warning: Non-zero offsets present. This is not yet supported and will be ignored.\n");
// Check that mapping is col=x row=y section=z
if (buffer.i[16] != 1 || buffer.i[17] != 2 || buffer.i[18] != 3) {
mprinterr("Error: Currently only support cols=X, rows=Y, sections=Z\n");
return 1;
}
if (buffer.i[24] != 0) {
mprintf("Warning: Skew information present but not yet supported and will be ignored.\n");
return 1;
}
// Read 10 80 character text labels
char Labels[801];
Labels[800] = '\0';
infile.Read( Labels, 200*wSize );
mprintf("\t%s\n", Labels);
// Symmetry records: operators separated by * and grouped into 'lines' of 80 characters
int NsymmRecords = buffer.i[23] / 80;
if (NsymmRecords > 0) {
char symBuffer[81];
mprintf("\t%i symmetry records.\n", NsymmRecords);
for (int ib = 0; ib != NsymmRecords; ib++) {
infile.Gets( symBuffer, 80 );
mprintf("\t%s\n", symBuffer);
}
}
// Add grid data set. Default to float for now.
DataSet* gridDS = datasetlist.AddSet( DataSet::GRID_FLT, dsname, "GRID" );
if (gridDS == 0) return 1;
DataSet_GridFlt& grid = static_cast<DataSet_GridFlt&>( *gridDS );
// Allocate grid from dims and spacing. FIXME OK to assume zero origin?
if (grid.Allocate_N_O_Box( buffer.i[7], buffer.i[8], buffer.i[9],
Vec3(0.0), Box(buffer.f + 10) ) != 0)
{
mprinterr("Error: Could not allocate grid.\n");
return 1;
}
// FIXME: Grids are currently indexed so Z is fastest changing.
// Should be able to change indexing in grid DataSet.
size_t mapSize = buffer.i[7] * buffer.i[8] * buffer.i[9];
mprintf("\tCCP4 map has %zu elements\n", mapSize);
mprintf("\tDensity: Min=%f Max=%f Mean=%f RMS=%f\n",
buffer.f[19], buffer.f[20], buffer.f[21], buffer.f[54]);
std::vector<float> mapbuffer( mapSize );
int mapBytes = mapSize * wSize;
int numRead = infile.Read( &mapbuffer[0], mapBytes );
if (numRead < 1) {
mprinterr("Error: Could not read CCP4 map data.\n");
return 1;
} else if (numRead < mapBytes)
mprintf("Warning: Expected %i bytes, read only %i bytes\n", mapBytes, numRead);
if (isBigEndian) endian_swap(&mapbuffer[0], mapSize);
// FIXME: Place data into grid DataSet with correct ordering.
int gidx = 0;
int NXY = buffer.i[7] * buffer.i[8];
for (int ix = 0; ix != buffer.i[7]; ix++)
for (int iy = 0; iy != buffer.i[8]; iy++)
for (int iz = 0; iz != buffer.i[9]; iz++) {
int midx = (iz * NXY) + (iy * buffer.i[7]) + ix;
grid[gidx++] = mapbuffer[midx];
}
infile.CloseFile();
return 0;
}
/** Load Karplus parameters from input file.
* Expected format:
* - {type}<+|-| ><a[4]><+|-| ><b[4]><+|-| ><c[4]><+|-| ><d[4]><A[6]><B[6]><C[6]>{<D[6]>}
* <reslabel[4]>*
* \return 0 on success, 1 on error
*/
int Action_Jcoupling::loadKarplus(std::string filename) {
char buffer[512],residue[5];
char *end, *ptr;
int i;
CpptrajFile KarplusFile;
karplusConstant KC;
karplusConstantList* currentResList=0;
std::string CurrentRes;
karplusConstantMap::iterator reslist;
if (filename.empty()) {
mprinterr("Error: jcoupling: Could not find Karplus parameter file.\n");
return 1;
}
if (KarplusFile.OpenRead( filename )) {
mprinterr("Error: jcoupling: Could not read Karplus parameter file %s\n",
filename.c_str());
mprinterr("Error: Ensure the file exists and is readable.\n");
return 1;
}
// residue is only for reading in 4 chars for residue names
residue[4]='\0';
// Read through all lines of the file
while (KarplusFile.Gets(buffer,512)==0) {
// Skip newlines and comments
if (buffer[0]=='\n' || buffer[0]=='#') continue;
ptr=buffer;
// First char is optional type. If optional type is C, then the Karplus
// function specified in Perez et al. JACS (2001) 123 will be used, and
// A, B, and C will be taken as C0, C1, and C2.
if(ptr[0]=='C') {
KC.type=1;
ptr++;
} else {
KC.type=0;
}
// Read atom names with optional preceding character (+, -)
for (i=0; i<4; i++) {
if (*ptr=='+') KC.offset[i]=1;
else if (*ptr=='-') KC.offset[i]=-1;
else KC.offset[i]=0;
++ptr;
char *endchar = ptr + 4;
char savechar = *endchar;
*endchar = '\0';
KC.atomName[i] = ptr;
*endchar = savechar;
ptr += 4;
//mprintf("DEBUG:\tAtomName %i [%s]\n",i,KC.atomName[i]);
}
// Read parameters
// NOTE: Using sscanf here instead of atof since the 4th parameter is
// optional, behavior is undefined for accessing uninitialized
// portion of buffer.
i = sscanf(ptr, "%6lf%6lf%6lf%6lf",KC.C,KC.C+1,KC.C+2,KC.C+3);
if (i<3) {
mprintf("Error: jcoupling: Expected at least 3 Karplus parameters, got %i\n",i);
mprintf(" Line: [%s]\n",buffer);
return 1;
} else if (i==3) KC.C[3]=0.0;
KC.C[3]*=Constants::DEGRAD;
// Place the read-in karplus constants in a map indexed by residue name
// so that all karplus constants for a given residue are in one place.
KarplusFile.Gets(buffer,512);
// end will hold the end of the read-in buffer string
end = buffer + strlen(buffer);
for (ptr = buffer; ptr < end; ptr+=4) {
if (*ptr=='\n') continue;
residue[0] = ptr[0];
residue[1] = ptr[1];
residue[2] = ptr[2];
residue[3] = ptr[3];
CurrentRes.assign(residue);
//mprintf("DEBUG:\t[%s]\n",CurrentRes.c_str());
reslist = KarplusConstants_.find(CurrentRes);
if (reslist == KarplusConstants_.end() ) {
// List does not exist for residue yet, create it.
currentResList = new karplusConstantList;
KarplusConstants_.insert( reslist,
std::pair<std::string,karplusConstantList*>(
CurrentRes,currentResList) );
} else
// Retrieve list for residue.
currentResList = (*reslist).second;
currentResList->push_back(KC);
++Nconstants_;
} // END loop over residues in residue line
} // END Gets over input file
KarplusFile.CloseFile();
// DEBUG - Print out all parameters
if (debug_>0) {
mprintf(" KARPLUS PARAMETERS:\n");
for (reslist=KarplusConstants_.begin(); reslist!=KarplusConstants_.end(); ++reslist)
{
mprintf("\t[%4s]\n",(*reslist).first.c_str());
for (karplusConstantList::iterator kc = currentResList->begin();
kc != currentResList->end(); ++kc)
{
mprintf("\t\t%1i",(*kc).type);
mprintf(" %4s",*((*kc).atomName[0]));
mprintf(" %4s",*((*kc).atomName[1]));
mprintf(" %4s",*((*kc).atomName[2]));
mprintf(" %4s",*((*kc).atomName[3]));
mprintf(" %i %i %i %i",(*kc).offset[0],(*kc).offset[1],(*kc).offset[2],(*kc).offset[3]);
mprintf(" %6.2lf %6.2lf %6.2lf %6.2lf\n",(*kc).C[0],(*kc).C[1],(*kc).C[2],(*kc).C[3]);
}
}
}
return 0;
}